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Kaiser Permanente starts the Autism Family Biobank Study

10 Aug

Kaiser Permanente has a long history of autism research. They’ve performed a number of epidemiology studies, including many on environmental risk factors and also the recent study on The health status of adults on the autism spectrum. They have recently embarked on a large study, the Kaiser Permanente Autism Family Biobank Study.

Sign up online
Study Flyer

You can also find picture books (social stories) for the sample donation process on the Autism Family Biobank website.

From the FAQ for the study, What is the KP Autism Family Biobank?

The KP Autism Family Biobank is a study of Kaiser Permanente Northern California children and young adults with Autism Spectrum Disorder (ASD) and their biological parents. The
study seeks to enroll 5,000 affected children plus their parents (for a total of 15,000 participants) to create a collection of genetic material and information for future research. Dr. Lisa Croen is the principal investigator of the study.

Autism genetics has turned out to be a very complex question. There’s no single “autism gene” but autism clearly has a large genetic component.

What does that mean in practical terms? We need a lot of data to understand the question of autism genetics. And that’s a big piece of what this study will do: bring a lot of data to bear. And not just genetic data. This is a key part of this study and can’t be stressed enough. Kaiser provides healthcare. They have electronic records on their patients. And these patients are the pool from which they will draw their study subjects.

Or to put it simply–they will be able to not only say, “these genes are associated with autism” but “these genes are associated with autism and low verbal skills, while these other genes are associated with autism and regression.” (to give a hypothetical example).

To do this they need a lot of people to participate. They are going to get 5000 autistic kids involved. And they won’t stop there: they will also include parents. That makes 15,000 participants. Not all genes are inherited. With the parents involved, Kaiser can can see if genes associated with autism are inherited or not.

Now many parents will ask (and it’s a valid question), “OK, what will this do for my kid?” It takes time (not a lot, but some) to participate and lots of kids don’t like doctor visits. But consider this: genetics helps people understand biology. With a better understanding of biology, one can make progress towards treatments. There’s a reason why some of the treatments proposed for autism came from research in Fragile-X. People have spent a lot of time studying this genetic condition and that focus has led to proposed treatments.

Or to put the short version of the message out–this isn’t just another genetics study. It’s bigger (15,000 people!) and brings a lot of value with the clinical data that Kaiser has. There’s a chance to have a big impact to better the lives of autistics. If you are a Kaiser member in the study area, please consider participating.

Links and recent news:

Sign up online
First KP Members Join Autism Family Biobank
Kaiser to look for autism’s causes in large-scale study
Study Flyer

By Matt Carey

Disclosure: I serve on a community advisory board for Kaiser. It is a volunteer position (I.e. I get no pay) and will not benefit from this study any more than anyone else in the autism community. And the decision to conduct this study was made before I became involved with Kaiser.

New Study: Most genetic risk for autism resides with common variation

23 Jul

A new large study on autism genetics just came out: Most genetic risk for autism resides with common variation. The study is in Nature Genetics, one of the top journals.

The study is the latest in the evolved view of autism genetics. Contrary to political statements made by some groups, autism genetics is not about searching for a single “autism gene”. Here’s a quote from the CNN Blog that makes this clear:

Chris Gunter, an autism researcher at the Marcus Autism Center and professor at the Emory University School of Medicine, says the findings of this study are similar to those reported in other studies.

“There is no one gene for autism,” Gunter said. “Instead there are many different genetic variations which each contribute a little bit to the risk of developing the group of symptoms we diagnose as autism.”

No single autism gene. You might carry one or more genes which are associated with autism and not be autistic. But the more you have, the more your risk goes up. It may be linear: each variant has a “score” and you add them up and if your score is very high, you are autistic. Or it may be nonlinear: some genes in combination may create a greater risk than the sum of their individual risks. I don’t think they understand or have cataloged the genes well enough to say.

The researchers in this current paper are estimating about 60% of autism risk is genetic. Here’s a graphic showing the breakdown of the various risks–different types of genes (common genes that are inherited, rare genes that are inherited, new (de novo) mutations, etc.):


What does this mean for the future of autism research? It means that continuing to look at both genetics and environmental risk factors is valuable. As I’ve said before, from my perspective if autism risk is 10% genetic or 90% genetic, you still need to apply resources to both genetics and environmental risk factors.

Now to answer the more mundane questions. What does this mean for the vaccine epidemic? You can’t have a genetic epidemic (not really true, but good enough for this discussion)! This doesn’t fit with the idea that about 99% of autism is now caused by vaccines.

Yep. These data are yet another reason why your idea doesn’t work.

But isn’t this just blaming the mothers?

I’m always amazed when that argument comes up on autism genetics. And, yes, it does come up. Your children’s genetic makeup is neither a source of pride nor of blame. You really didn’t have any say in the matter. You didn’t create nor change your genes, how can you be blamed for the genes that your child inherits?

Won’t genetic research lead to aborting babies?

Maybe. If it does, it will be much different than the current situation with Down Syndrome. Autism doesn’t have many examples of single-genes, as this study points out. There have already been groups claiming to be working on tests involving multiple genes and autism risk scores.

Does this mean that the story is finished? That we have the last answer about how much risk is genetic and how much is environmental?

No. There will be more papers and more estimates. These are tough questions and knowledge evolves.

Here is the paper’s abstract:

A key component of genetic architecture is the allelic spectrum influencing trait variability. For autism spectrum disorder (herein termed autism), the nature of the allelic spectrum is uncertain. Individual risk-associated genes have been identified from rare variation, especially de novo mutations. From this evidence, one might conclude that rare variation dominates the allelic spectrum in autism, yet recent studies show that common variation, individually of small effect, has substantial impact en masse. At issue is how much of an impact relative to rare variation this common variation has. Using a unique epidemiological sample from Sweden, new methods that distinguish total narrow-sense heritability from that due to common variation and synthesis of results from other studies, we reach several conclusions about autism’s genetic architecture: its narrow-sense heritability is ∼52.4%, with most due to common variation, and rare de novo mutations contribute substantially to individual liability, yet their contribution to variance in liability, 2.6%, is modest compared to that for heritable variation.

By Matt Carey

Embryo screening to reduce autism risk: it’s not in the future. It’s now

28 Dec

A news article on screening of embryos came out last week and it was picked up under various titles by various news outlets.

From Australia and New Zealand

Why IVF parents are choosing girls over boys, which google news also listed under Parents call for embryo screening to cut risks.

IVF parents choosing girls over boys

And a different take

Parents Worldwide Prefer Girls To Boys: Will India And China Learn?

From India

Why girls are preferred over boys by IVF parents

Here’s a quote from one of the stories:

Figures from one of Sydney’s top IVF clinics show about one in 20 parents seeking embryo screening are looking to have a female baby to reduce their risk of autism.

Australia does not allow for gender selection of embryos. One can’t tell the IVF team to pick male or female embryos. But one can ask for genetic screening.

University of Sydney senior lecturer in bioethics Chris Jordens said autism had a strong genetic basis, so it was within the guidelines.

And the trend towards genetic screening is strong and building in the US.

At a recent conference in Chicago, he saw a number of United States IVF providers offering parents without the conditions tests for between 180 and 600 common gene mutations, such as the BRCA ”breast cancer” genes.

Gender selection to reduce autism risk is about the most basic, the most crude, genetic screening one could imagine. But it’s real and it’s happening.

The concept of autism prevention through genetic screening, either in IVF or in selective abortions, has been a major ethical question with the push for genetics research in autism in the past decade.

The first step in guiding our societies towards an ethical approach to genetic testing is to present autism accurately. This is one reason why I and others speak out when groups such as Autism Speaks or some parent “advocates” present autism with phrases such as as “These families are not living” or “Life is lived…in despair”. Is life harder, more challenging for my kid? Absolutely. But what message are we sending to prospective parents when we tell them that their lives will be lived in despair or they will no longer be living if they have an autistic child? We are telling them to do whatever they can to avoid having an autistic child. We are telling them to pick and chose their embryos. We are telling them to selectively abort. We are telling the autistics of today that the perfect world (in the view of the majority) is one without them.

My kid and other autistics, children and adults, deserve life. They deserve the right to pursue happiness. Disabled does not equate to despair.

This is why, Autism Speaks, when you portray my kid as less, my life as not lived, I and others will speak out. Autism Speaks, it’s time you started listening.

By Matt Carey

The Amish may not be a great population for a vaccinated/unvaccinated study

10 Aug

The recent attempt to legislate brought back the subject of the Amish, vaccination and autism. It’s an old idea, made popular by a journalist whose work was, shall we say, less than complete.

House Resolution 1757 (still stuck in committee) states:

” Target Populations- The Secretary shall seek to include in the study under this section populations in the United States that have traditionally remained unvaccinated for religious or other reasons, which populations may include Old Order Amish…”

Whenever the Amish are brought forward as a population for vaccinated/unvaccinated studies, people present many reasons why such an idea lacks rigor.

1) The Amish do vaccinate. They have no prohibition against vaccination. (i.e. the statement that “because the Amish have a religious exemption from vaccination” is incorrect).

2) “The” Amish is a bit of a misnomer. Amish is more of a plural, as in a group of basically island populations which have been developing somewhat independently genetically for a few hundred years.

3) Talking about studying the Amish as though one has the right to just force them to submit is very disrespectful. And a bad assumption. One does not tell a community that they have to be study subjects. One asks. The Amish may very well not want the entire population screened for autism.

There are more arguments. Valid arguments. But without some cold, hard, numbers the response that usually comes up is, “Ah, you are afraid of what we will find!”

No, if one is going to do a study, one should be rigorous. One should get as close to the correct answer as possible. Studying the Amish as an “unvaccinated” population with “no” (or little) autistic subpopulation is to start out with little chance for success.

But how about some cold, hard numbers (I mean, beside from the fact that the Amish vaccinate and there are autistic Amish).

Here’s a talk presented this summer by the DDC Clinic in Ohio. This clinic is following the model of the cleverly hidden “Clinic For Special Children” that a certain journalist failed to contact before publishing his conclusions. In the description of the Clinic you will find:

A 501(c) (3) non-profit organization located in
Middlefield of Ohio, Geauga Amish settlement
• Total population ~95,000, Amish ~14,000 (15%)
• 50% of developmental disabilities are from Amish
• One hour (but a world) away from world class healthcare

Yes, they are 15% of the local population but account for about 50% of the developmentally disabled population for their community.

In other words, the prevalence of developmental disability is more than five times that of the general population.

Do you still want to compare this population for long term health outcomes and vaccination status? Do you want to say, “hey, here’s a population that doesn’t vaccinate and they have more developmental disability than the rest of the population?”

That’s what people have been pointing out for years in stating that genetically the Amish are somewhat distinct from the rest of the U.S. population. The proposed study will run into big problems.

Why does the Clinic for Special Children (and similar clinics) exist? They aren’t just there because the Amish are likely to be underserved in general since they lack insurance (which, I’ve been told, is something the Amish avoid). The Clinic’s mission statement is:

The Clinic for Special Children was established in 1989 as a non-profit medical service for Amish and Mennonite children with genetic disorders. The Clinic serves children by translating advances in genetics into timely diagnoses and accessible, comprehensive medical care, and by developing better understanding of heritable diseases.

Again, they are a small, island-like population. Many genetic conditions are more common in their communities. Many are metabolic conditions. (Dr. Morton’s talk at the conference was “Approach to Care for Patients with Metabolic Disorders”). Conditions which put people at greater risk of harm from infections, hence the reason that people have been working to increase vaccine uptake in the Amish over the past 3 decades.

The Clinic for Special Children has been an example of how focusing on genetic conditions can have major impacts on the well being of those with the conditions. Over the past 30 years, the Clinic has pioneered efforts which have resulted in better health and longer lives for their patients. Too often we hear in the autism communities that genetic conditions mean “no hope”.

I’ll leave you with the words of Dr. Holmes Morton of the Clinic for Special Children. Words from the Clinic’s main page:

“Special children are not just interesting medical problems, subjects of grants and research. Nor should they be called burdens to their families and communities. They are children who need our help, and if we allow them to, they will teach us compassion. They are children who need our help, and if we allow them to, they will teach us love. If we come to know these children as we should, they will make us better scientists, better physicians, and thoughtful people.”

By Matt Carey

Comment on: A Danish population-based twin study on autism spectrum disorders.

12 May

There has been much discussion of twin studies in autism research for a long time. The reason is that if is found that “identical” (monozygotic) twins are often both autistic, that points to genetics as a major influence on the development of autism. For many years it was thought that this rate, the concordance, was about 90%. In other words, if one child is autistic, 90% of the time the other child is autistic. This was based on a number of older, small studies. More recently, a relatively large study showed a lower concordance: about 77% for ASD and 60% for autism. From this the authors claimed that the genetic contribution to autism risk was lower than previously thought, and that the environmental contribution was higher (about 55% environmental contribution).

A study just out from Denmark claims a concordance more in line with the older studies–95%. In A Danish population-based twin study on autism spectrum disorders., the authors write:

Genetic epidemiological studies of Autism Spectrum Disorders (ASDs) based on twin pairs ascertained from the population and thoroughly assessed to obtain a high degree of diagnostic validity are few. All twin pairs aged 3-14 years in the nationwide Danish Twin Registry were approached. A three-step procedure was used. Five items from the “Child Behaviour Checklist” (CBCL) were used in the first screening phase, while screening in the second phase included the “Social and Communication Questionnaire” and the “Autism Spectrum Screening Questionnaire”. The final clinical assessment was based on “gold standard” diagnostic research procedures including diagnostic interview, observation and cognitive examination. Classification was based on DSM-IV-TR criteria. The initial sample included 7,296 same-sexed twin pairs and, after two phases of screening and clinical assessment, the final calculations were based on 36 pairs. The probandwise concordance rate for ASD was 95.2 % in monozygotic (MZ) twins (n = 13 pairs) and 4.3 % in dizygotic (DZ) twins (n = 23 pairs). The high MZ and low DZ concordance rate support a genetic aetiology to ASDs.

This study is relatively small with only 13 “identical” twin pairs. Also, the concordance for “fraternal” (dizygotic) twins is relatively low at 4.3%. Sibling concordance is estimated at about 20%, so 4.3% raises a bit of a red flag. Of course the recent larger twin study is not without some controversy itself.

In the end, I doubt this new study will have much influence on the online parent community discussions (which are in themselves far from the most productive or important discussions on the topic. Just the apparently most vocal). We are left with there being some genetic contribution and some environmental contribution to autism risk. In other words, it remains important to put effort into both areas of research.

By Matt Carey

Spontaneous Gene Glitches Linked to Autism Risk with Older Dads

4 Apr

Below is a press release from the National Institutes of Health (NIH) in the U.S.. on recently published studies on autism risk. These are the studies mentioned by NIMH Director and IACC chair Thomas Insel in his article “The New Genetics of Autism – Why Environment Matters“.

Spontaneous Gene Glitches Linked to Autism Risk with Older Dads
Non-Inherited Mutations Spotlight Role of Environment – NIH-Supported Study, Consortium

Researchers have turned up a new clue to the workings of a possible environmental factor in autism spectrum disorders (ASDs): fathers were four times more likely than mothers to transmit tiny, spontaneous mutations to their children with the disorders. Moreover, the number of such transmitted genetic glitches increased with paternal age. The discovery may help to explain earlier evidence linking autism risk to older fathers.

The results are among several from a trio of new studies, supported in part by the National Institutes of Health, finding that such sequence changes in parts of genes that code for proteins play a significant role in ASDs. One of the studies determined that having such glitches boosts a child’s risk of developing autism five to 20 fold.

Taken together, the three studies represent the largest effort of its kind, drawing upon samples from 549 families to maximize statistical power. They reveal sporadic mutations widely distributed across the genome, sometimes conferring risk and sometimes not. While the changes identified don’t account for most cases of illness, they are providing clues to the biology of what are likely multiple syndromes along the autism spectrum.

“These results confirm that it’s not necessarily the size of a genetic anomaly that confers risk, but its location – specifically in biochemical pathways involved in brain development and neural connections. Ultimately, it’s this kind of knowledge that will yield potential targets for new treatments,” explained Thomas, R. Insel, M.D., director of the NIH’s National Institute of Mental Health (NIMH), which funded one of the studies and fostered development of the Autism Sequencing Consortium, of which all three groups are members.

Multi-site research teams led by Mark Daly, Ph.D., of the Harvard/MIT Broad Institute, Cambridge, Mass., Matthew State, M.D., Ph.D., of Yale University, New Haven, Conn., and Evan Eichler, Ph.D., of the University of Washington, Seattle, report on their findings online April 4, 2012 in the journal Nature.

The study by Daly and colleagues was supported by NIMH – including funding under the American Recovery and Reinvestment Act. The State and Eichler studies were primarily supported by the Simons Foundation Autism Research Initiative. The studies also acknowledge the NIH’s National Human Genome Research Institute, National Heart Lung and Blood Institute, and National Institute on
Child Health and Human Development and other NIH components.

All three teams sequenced the protein coding parts of genes in parents and an affected child – mostly in families with only one member touched by autism. One study also included comparisons with healthy siblings. Although these protein-coding areas represent only about 1.5 percent of the genome, they harbor 85 percent of disease-causing mutations. This strategy optimized the odds for detecting the few spontaneous errors in genetic transmission that confer autism risk from the “background noise” generated by the many more benign mutations.

Like larger deletions and duplications of genetic material previously implicated in autism and schizophrenia, the tiny point mutations identified in the current studies are typically not inherited in the conventional sense – they are not part of parents’ DNA, but become part of the child’s DNA. Most people have many such glitches and suffer no ill effects from them. But evidence is building that such mutations can increase risk for autism if they occur in pathways that disrupt brain development.
State’s team found that 14 percent of people with autism studied had suspect mutations – five times the normal rate. Eichler and colleagues traced 39 percent of such mutations likely to confer risk to a biological pathway known to be important for communications in the brain.

Although Daly and colleagues found evidence for only a modest role of the chance mutations in autism, those pinpointed were biologically related to each other and to genes previously implicated in autism.

The Eichler team turned up clues to how environmental factors might influence genetics. The high turnover in a male’s sperm cells across the lifespan increases the chance for errors to occur in the genetic translation process. These can be passed-on to the offspring’s DNA, even though they are not present in the father’s DNA. This risk may worsen with aging. The researchers discovered a four-fold marked paternal bias in the origins of 51 spontaneous mutations in coding areas of genes that was positively correlated with increasing age of the father. So such spontaneous mutations could account for findings of an earlier study that found fathers of boys with autism were six times – and of girls 17 times – more likely to be in their 40’s than their 20’s.

“We now have a path forward to capture a great part of the genetic variability in autism – even to the point of being able to predict how many mutations in coding regions of a gene would be needed to account for illness,” said Thomas Lehner, Ph.D., chief of the NIMH Genomics Research Branch, which funded the Daly study and helped to create the Autism Sequencing Consortium. “These studies begin to tell a more comprehensive story about the molecular underpinnings of autism that integrates previously disparate pieces of evidence.”

Sanders SJ, Murtha MT, Gupta AR, Murdoch JD, Raubeson MJ, Willsey AJ, Ercan-Sencicek AG, DiLullo NM, Parikshak NN, Stein JL, Walker MF, Ober GT, Teran NA, Song Y, El-Fishawy P, Murtha RC, Choi M, Overton JD, Bjornson RD, Carriero NJ, Meyer KA, Bilguvar K, Mane SM, Sestan N, Lifton RP, Günel M, Roeder K, Geschwind DH, Devlin B, State MW. De novo mutations revealed by whole-exome sequencing are strongly associated with autism. April 5, 2012. Nature.
O’Roak BJ, Vives L, Girirajan S, Karakoc E, Krumm N, Coe BP, Levy R, Ko A, Lee C, Smith JD, Turner EH, Stanaway IB, Vernot B, Malig M, Baker C, Reilly B, Akey JM, Borenstein E, Rieder MJ, Nickerson DA, Bernier R, Shendure J, Eichler EE. Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature. April 5, 2012.
Neale BM, Kou Y, Liu L, Ma’ayan A, Samocha KE, Sabo A, Lin CF, Stevens C, Wang LS, Makarov V, Polak P, Yoon S, Maguire J, Crawford EL, Campbell NG, Geller ET, Valladares O, Schafer C, Liu H, Zhao T, Cai G, Lihm J, Dannenfelser R, Jabado O, Peralta Z, Nagaswamy U, Muzny D, Reid JG, Newsham I, Wu Y, Lewis L, Han Y, Voight BF, Lim E, Rossin E, Kirby A, Flannick J, Fromer M, Shair K, Fennell T, Garimella K, Banks E, Poplin R, Gabriel S, DePristo M, Wimbish JR, Boone BE, Levy SE, Betancur C, Sunyaev S, Boerwinkle E, Buxbaum JD, Cook EH, Devlin B, Gibbs RA, Roeder K, Schellenberg GD, Sutcliffe JS, Daly MJ. Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature. April 5, 2012.
The mission of the NIMH is to transform the understanding and treatment of mental illnesses through basic and clinical research, paving the way for prevention, recovery and cure. For more information, visit the NIMH website.
About the National Institutes of Health (NIH): NIH, the nation’s medical research agency, includes 27 Institutes and Centers and is a component of the U.S. Department of Health and Human Services. NIH is the primary federal agency conducting and supporting basic, clinical, and translational medical research, and is investigating the causes, treatments, and cures for both common and rare diseases. For more information about NIH and its programs, visit the NIH website.

Thomas Insel: The New Genetics of Autism – Why Environment Matters

4 Apr

Thomas Insel is the director of the National Institute of Mental Health (NIMH) and the chair of the Interagency Autism Coordinating Committee (IACC) in the U.S..

His article can be found here (The New Genetics of Autism – Why Environment Matters) and I have quoted it in full bellow. (As a government publication I feel that it is appropriate to use the entire piece):

Last week’s autism news was about prevalence. The CDC reported a 78 percent increase in autism prevalence since 2002. This week’s autism news is about genetics—three papers in Nature describe new genes associated with autism. For many people, these two stories seem contradictory or, at best, unrelated. Increasing prevalence suggests environmental factors like chemicals and microbes changing over the past decade, whereas genes change over generations. Why is anyone looking for genetic causes when there is such a rapid increase in prevalence? Shouldn’t every research dollar be invested in finding the environmental culprit rather than searching for rare gene variants?

The simple answer is that some autism is genetic. Autism, like schizophrenia and mood disorders, includes many syndromes. Indeed, we should probably speak of the “autisms.” Some of these autisms are single gene disorders, such as Fragile X, tuberous sclerosis, and Rett syndrome. While these rare genetic disorders account for less than 5 percent of children within the autism spectrum, children with any of these disorders are at high risk for autism, roughly a 30-fold higher risk than the general population and higher than any of the other known risk factors. Recent genomics research has discovered that many children diagnosed within the autism spectrum have other genetic mutations that have not yet been designated as named syndromes. Each of these mutations is rare, but in aggregate they may account for 10 – 20 percent or more of what we have been calling the autisms.1

The new papers published today in Nature use an approach called whole exome sequencing, mapping every base of DNA across the exome—the 1.5 percent of the genome known to code for protein. The three research groups are members of the Autism Sequencing Consortium (ASC), an international team of autism genetics researchers. All three look for de novo or spontaneous mutations, changes in DNA sequence that are not found in either parent. Recent sequencing studies in the general population have demonstrated that each of us diverges genomically from our parents — the process of reproduction introduces variation even beyond the random mixture of the genomes we inherit from mom and dad. People with autism and schizophrenia are far more likely to have large de novo copy number variants, sometimes a million bases of DNA that are abnormally duplicated or deleted and not found in either parent.
These new papers go beyond the previous discovery of de novo copy number variants to identify de novo single base changes associated with autism. This is tough sailing because there are so many of these changes in all of us and most of these single base changes have no impact. These studies tried to improve the odds of success by focusing on individuals from families with no one else affected (these are called “simplex” families), and sometimes comparing the individual with autism to a sibling without autism. The results are intriguing.

There is no breakthrough or single gene that is a major new cause of autism. But the role of genetics becomes even more evident when these single base changes are considered. For instance, an individual with autism is nearly 6-fold more likely to have a functional variant in genes expressed in the brain. Sanders et al. estimate as many as 14 percent of affected individuals have such a risk variant.2 This 14 percent is in addition to the 10–20 percent with a large copy number variant or identified genetic syndrome. O’Roak et al. find that 39 percent of these variants are related to a specific biochemical pathway, important for brain signaling.3 And Neale et al., while cautioning that the net effect of all of these changes still leave much of the risk for autism unexplained, note the roles of a few specific genes as genuine risk factors.4

Stepping back from this flood of genomic information, what is most important? First, these reports along with previous publications confirm that genetic risk is both complex and substantial. While individual genes appear to confer limited risk, the aggregate effect of spontaneous coding mutations across the genome is now estimated to increase the risk of autism by 5–20-fold.4 Complex genetics does not mean modest effects.

Second, the kinds of small and large genetic changes associated with autism are common in everyone. Risk is conferred not by the size of the mutation or the number of mutations (we all have many) but by the location. Increasingly, we see that interference with the genes involved in development of synapses confer risk; a similar change upstream or downstream does not.
A third point takes us back to the questions we started with. It is important to understand that de novo mutations may represent environmental effects. In other words, environmental factors can cause changes in our DNA that can raise the risk for autism and other disorders. One of these papers reports that spontaneous changes are four times more likely to show up in paternally inherited DNA and are correlated with paternal age.2 The father’s germline, his sperm cells, turn over throughout the lifespan. Presumably, with advancing paternal age, there are a greater number of spontaneous mutations and a greater likelihood that some of these will affect risk genes. Environmental factors and exposures can cause sperm cells to develop mutations that are not found in the father’s somatic, or body cell, DNA, but these new, spontaneous mutations can be passed to the next generation, raising the risk for developing autism. In the initial report of the relationship between autism and paternal age, boys with autism were 6-fold more likely to have a father in his 40s vs his 20s. In girls with autism, this difference went up to 17-fold.5 Paternal age has, of course, increased in the past few decades. This does not explain the increasing prevalence of autism, but it may contribute.

Is autism genetic or environmental? These new studies suggest it can be both. Genetics will not identify the environmental factors, but it may reveal some of the many syndromes within the autism spectrum (as in other neurodevelopmental disorders), it can define risk (as in other medical disorders), and it should yield clues to the biology of autism (revealing potential targets for new treatments). These three new papers on spontaneous mutations are an important milestone in a long journey. In parallel we need to find environmental factors, recognizing that there will be many causes for the autisms and many roads to find them.

Finally, an unavoidable insight from these new papers is that autism even when genetic may be spontaneous and not inherited in the sense that one or both parents carry some reduced form of the syndrome. Perhaps this insight will finally reduce the “blame the parents” legacy perpetuated for too long in the absence of scientific evidence.

1Geschwind DH. Genetics of autism spectrum disorders. Trends Cogn Sci. 2011 Sep;15(9):409-16. Epub 2011 Aug 18. PubMed PMID: 21855394.1
2Sanders SJ, Murtha MT, Gupta AR, Murdoch JD, Raubeson MJ, Willsey AJ, Ercan-Sencicek AG, DiLullo NM, Parikshak NN, Stein JL, Walker MF, Ober GT, Teran NA, Song Y, El-Fishawy P, Murtha RC, Choi M, Overton JD, Bjornson RD, Carriero NJ, Meyer KA, Bilguvar K, Mane SM, Sestan N, Lifton RP, Günel M, Roeder K, Geschwind DH, Devlin B, State MW. De novo mutations revealed by whole-exome sequencing are strongly associated with autism. April 5, 2012. Nature.
3O’Roak BJ, Vives L, Girirajan S, Karakoc E, Krumm N, Coe BP, Levy R, Ko A, Lee C, Smith JD, Turner EH, Stanaway IB, Vernot B, Malig M, Baker C, Reilly B, Akey JM, Borenstein E, Rieder MJ, Nickerson DA, Bernier R, Shendure J, Eichler EE. Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature. April 5, 2012.
4Neale BM, Kou Y, Liu L, Ma’ayan A, Samocha KE, Sabo A, Lin CF, Stevens C, Wang LS, Makarov V, Polak P, Yoon S, Maguire J, Crawford EL, Campbell NG, Geller ET, Valladares O, Schafer C, Liu H, Zhao T, Cai G, Lihm J, Dannenfelser R, Jabado O, Peralta Z, Nagaswamy U, Muzny D, Reid JG, Newsham I, Wu Y, Lewis L, Han Y, Voight BF, Lim E, Rossin E, Kirby A, Flannick J, Fromer M, Shair K, Fennell T, Garimella K, Banks E, Poplin R, Gabriel S, DePristo M, Wimbish JR, Boone BE, Levy SE, Betancur C, Sunyaev S, Boerwinkle E, Buxbaum JD, Cook EH, Devlin B, Gibbs RA, Roeder K, Schellenberg GD, Sutcliffe JS, Daly MJ. Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature. April 5, 2012.
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Lack of association between autism and four heavy metal regulatory genes

30 Jul

One question that has been discussed for some time is the hypothesized role of mercury as a potential cause of autism. The basic idea is that administrative prevalences of autism went up coincident with increases in mercury exposure from vaccines. Plus, it was asserted that autism symptoms are similar to the symptoms of mercury poisoning (they aren’t).

Part of the mercury model held that there could be a genetic susceptibility to mercury in a subset of children.

Researchers at Vanderbilt University have explored the question by testing autistics for genes involved in how the body processes mercury. They did not find any link between the four genes they screened and autism.

Of course one could argue that some other gene or genes are important. One would then need to explain why mercury exposure from vaccines does not increase the risk of autism.

The paper:
Lack of association between autism and four heavy metal regulatory genes.

Here’s the abstract.

Neurotoxicology. 2011 Jul 20. [Epub ahead of print]
Lack of association between autism and four heavy metal regulatory genes.
Owens SE, Summar ML, Ryckman KK, Haines JL, Reiss S, Summar SR, Aschner M.
Department of Pediatric Toxicology, Vanderbilt University School of Medicine, Nashville, TN, USA.
Autism is a common neurodevelopmental disorder with genetic and environmental components. Though unproven, genetic susceptibility to high mercury (Hg) body burden has been suggested as an autism risk factor in a subset of children. We hypothesized that exposure to “safe” Hg levels could be implicated in the etiology of autism if genetic susceptibility altered Hg’s metabolism or intracellular compartmentalization. Genetic sequences of four genes implicated in the transport and response to Hg were screened for variation and association with autism. LAT1 and DMT1 function in Hg transport, and Hg exposure induces MTF1 and MT1a. We identified and characterized 74 variants in MT1a, DMT1, LAT1 and MTF1. Polymorphisms identified through screening 48 unrelated individuals from the general and autistic populations were evaluated for differences in allele frequencies using Fisher’s exact test. Three variants with suggestive p-values <0.1 and four variants with significant p-values <0.05 were followed-up with TaqMan genotyping in a larger cohort of 204 patients and 323 control samples. The pedigree disequilibrium test was used to examine linkage and association. Analysis failed to show association with autism for any variant evaluated in both the initial screening set and the expanded cohort, suggesting that variations in the ability of the four genes studied to process and transport Hg may not play a significant role in the etiology of autism.

Genetic explanation for why autism (apparently) affects more males than females

22 Feb

Firstly we should start by saying there is a strand to the debate that strongly indicates that autism in females is heavily underdiagnosed.

That said, interesting new research emerges from George Washington University.

The team basically looked at a gene implicated in autism called retinoic acid-related orphan receptor-alpha, or RORA (brains of autistic people make less of it than usual) and bathed it in two things.

Firstly they bathed human brain cells in an oestrogen mix and secondly they bathed different brain cells in DHT. The oestrogen _enhanced_ RORA production whereas the DHT _supressed_ it.

This is not to downplay the role that underdiagnosis in females very probably plays but it does show how genes affect autism directly.

Get ready for the flood of fetal gene screening

21 Feb

In a recent article in Nature, Henry T. Greely, proposes that the time when prenatal genetic screening may be commonplace is closer than, well, I thought.

The world’s news media was buzzing last week after researchers showed that a blood test for mothers could detect Down’s syndrome in their fetuses[1]. Last month, two research groups independently published proof that the fetal genotype — the genetic status at a given locus — can be derived for thousands of sites from samples of fetal DNA with just a 10-millilitre blood draw from a pregnant woman[2, 3].

[1] Chiu, R. W. K. et al. Br. Med. J. doi: 10.1136/bmj.c7401 (2011).

[2] Lo, Y. M. D. et al. Sci. Transl. Med. 2, 61ra91 (2010).

[3] Fan, H. C. & Quake, S. R. Nature Precedings doi:10.1038/npre.2010.5373.1 (2010).

Until now, the main prenatal testing has been for Down Syndrome. It is not common:

Prenatal genetic testing has been clinically available since the late 1960s, but the costs, inconvenience and especially the miscarriage risks have limited its use. Each year, less than 2% of pregnant women in the United States undergo amniocentesis (in which a small amount of amniotic fluid containing fetal cells is taken for analysis) or chorionic villus sampling (CVS — in which fetal tissue is extracted from the placenta). Both procedures increase the risk of miscarriage. Until now, any given sample could be tested for only one or two conditions, typically chromosomal abnormalities such as trisomy 21, the cause of Down’s syndrome.

It is uncommon, but it is offered in high risk situations (older mothers). Since the test has been offered, the prevalence of Down Syndrome has dropped significantly. This in spite of the fact that older mothers are more common now.

Amniocentesis is obviously invasive, resulting in risk to the unborn child. But a blood draw would be a non-invasive prenatal genetic diagnosis (NIPD).

The potential of NIPD goes way beyond Rhesus screening. Two of the leading researchers in cell-free fetal DNA testing — Dennis Lo of the University of Hong Kong and Steve Quake of Stanford University in California — use different methods to analyse fetal cell-free DNA from maternal serum. Each has demonstrated the ability to detect aneuploidies — missing or extra chromosomes, such as in trisomy 21 (refs 5, 6). Last month, both researchers published proof that the fetal genotype could be derived for thousands of sites from cell-free fetal DNA2, 3 — demonstrating the possibility of using maternal blood to test for all fetal genetic traits.

The methods demonstrated are already interesting commercial firms:

Commercial firms are already interested. Sequenom in San Diego, California, is working with Lo; another, Artemis Health of Menlo Park, California, is working with Quake; and still others are also exploring the technology. For-profit development of these methods seems likely within five years, at least for chromosomal abnormalities, such as trisomy 21, and possibly for single-gene traits.

My insurance plan will pay for prenatal genetic testing, but not for genetic testing of a child. I find that thought a bit chilling.

Until now, prenatal genetic testing has been relatively uncommon. The ethics discussions have been largely academic. Important, but academic. The time for academic discussions of the ethics is drawing to a close.

Professional organizations, in medicine and in genetics, need to get involved, both in training their members about these technologies and in beginning to consider guidelines for their use, especially with regard to informed consent. Regulators, companies and consumer advocates need to be talking about pathways for assuring the safety, efficacy and quality of NIPD testing. In the United States, the Food and Drug Administration should start that process immediately. And it is time for ethics commissions, such as the US Presidential Commission for the Study of Bioethical Issues, to report on these issues.

Most importantly, we need to start conversations, between all those concerned, about the limits, if any, to place on this powerful technology. Whether we view NIPD gladly as a way to reduce human suffering, warily as a step towards a eugenic dystopia, or as a mix of both, we should agree that the better we prepare, the more likely we are to avoid the worst misuses of this potentially transformative technology.

What disabilities will eventually have genetic screening possible? How will we as a society take on the ethical challenges? If the drop in Down Syndrome is any indication, I think there is reason to take this discussion very seriously. Now.